OpenRaiser/Intern-Atlas huggingface dataset:
Efficient FPT algorithms for (strict) compatibility of unrooted phylogenetic trees
Venue: arXiv cs.DS 2016
Year: 2016

In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$ and without degree-2 nodes -- called the "species tree". One common approach for reconstructing a species tree consists in first constructing several phylogenetic trees from primary data (e.g. DNA sequences originating from some species in $X$), and then constructing a single phylogenetic tree maximizing the "concordance" with the input trees. The so-obtained tree is our estimation of the species tree and, when the input trees are defined on overlapping -- but not identical -- sets of labels, is called "supertree". In this paper, we focus on two problems that are central when combining phylogenetic trees into a supertree: the compatibility and the strict compatibility problems for unrooted phylogenetic trees. These problems are strongly related, respectively, to the notions of "containing as a minor" and "containing as a topological minor" in the graph community. Both problems are known to be fixed-parameter tractable in the number of input trees $k$, by using their expressibility in Monadic Second Order Logic and a reduction to graphs of bounded treewidth. Motivated by the fact that the dependency on $k$ of these algorithms is prohibitively large, we give the first explicit dynamic programming algorithms for solving these problems, both running in time $2^{O(k^2)} \cdot n$, where $n$ is the total size of the input.
Know When to Persist: Deriving Value from a Stream Buffer
Venue: arXiv cs.DS 2016
Year: 2016

We consider \textsc{Persistence}, a new online problem concerning optimizing weighted observations in a stream of data when the observer has limited buffer capacity. A stream of weighted items arrive one at a time at the entrance of a buffer with two holding locations. A processor (or observer) can process (observe) an item at the buffer location it chooses, deriving this way the weight of the observed item as profit. The main constraint is that the processor can only move {\em synchronously} with the item stream; as a result, moving from the end of the buffer to the entrance, it crosses paths with the item already there, and will never have the chance to process or even identify it. \textsc{Persistence}\ is the online problem of scheduling the processor movements through the buffer so that its total derived value is maximized under this constraint. We study the performance of the straight-forward heuristic {\em Threshold}, i.e., forcing the processor to "follow" an item through the whole buffer only if its value is above a threshold. We analyze both the optimal offline and Threshold algorithms in case the input stream is a random permutation, or its items are iid valued. We show that in both cases the competitive ratio achieved by the Threshold algorithm is at least $2/3$ when the only statistical knowledge of the items is the median of all possible values. We generalize our results by showing that Threshold, equipped with some minimal statistical advice about the input, achieves competitive ratios in the whole spectrum between $2/3$ and $1$, following the variation of a newly defined density-like measure of the input. This result is a significant improvement over the case of arbitrary input streams, since in this case we show that no online algorithm can achieve a competitive ratio better than $1/2$.
Distributed Nonlinear Observer with Robust Performance - A Circle Criterion Approach
Venue: arXiv cs.SY 2016
Year: 2016

In this paper, we present a distributed version of the KYP-Lemma with the goal to express the strictly positive real-property for a class of physically interconnected systems by a set of local LMI-conditions. The resulting conditions are subsequently used to constructively design distributed circle criterion estimators, which are able to collectively estimate an underlying linear system with a sector bounded nonlinearity.
CLEAR: Cross-Layer Exploration for Architecting Resilience - Combining Hardware and Software Techniques to Tolerate Soft Errors in Processor Cores
Venue: arXiv cs.AR 2016
Year: 2016

We present a first of its kind framework which overcomes a major challenge in the design of digital systems that are resilient to reliability failures: achieve desired resilience targets at minimal costs (energy, power, execution time, area) by combining resilience techniques across various layers of the system stack (circuit, logic, architecture, software, algorithm). This is also referred to as cross-layer resilience. In this paper, we focus on radiation-induced soft errors in processor cores. We address both single-event upsets (SEUs) and single-event multiple upsets (SEMUs) in terrestrial environments. Our framework automatically and systematically explores the large space of comprehensive resilience techniques and their combinations across various layers of the system stack (586 cross-layer combinations in this paper), derives cost-effective solutions that achieve resilience targets at minimal costs, and provides guidelines for the design of new resilience techniques. We demonstrate the practicality and effectiveness of our framework using two diverse designs: a simple, in-order processor core and a complex, out-of-order processor core. Our results demonstrate that a carefully optimized combination of circuit-level hardening, logic-level parity checking, and micro-architectural recovery provides a highly cost-effective soft error resilience solution for general-purpose processor cores. For example, a 50x improvement in silent data corruption rate is achieved at only 2.1% energy cost for an out-of-order core (6.1% for an in-order core) with no speed impact. However, selective circuit-level hardening alone, guided by a thorough analysis of the effects of soft errors on application benchmarks, provides a cost-effective soft error resilience solution as well (with ~1% additional energy cost for a 50x improvement in silent data corruption rate).
Symbolic Knowledge Extraction using Łukasiewicz Logics
Venue: arXiv cs.AI 2016
Year: 2016

This work describes a methodology that combines logic-based systems and connectionist systems. Our approach uses finite truth-valued Łukasiewicz logic, wherein every connective can be defined by a neuron in an artificial network. This allowed the injection of first-order formulas into a network architecture, and also simplified symbolic rule extraction. For that we trained a neural networks using the Levenderg-Marquardt algorithm, where we restricted the knowledge dissemination in the network structure. This procedure reduces neural network plasticity without drastically damaging the learning performance, thus making the descriptive power of produced neural networks similar to the descriptive power of Łukasiewicz logic language and simplifying the translation between symbolic and connectionist structures. We used this method for reverse engineering truth table and in extraction of formulas from real data sets.
Towards a Privacy Research Roadmap for the Computing Community
Venue: arXiv cs.CY 2016
Year: 2016

Great advances in computing and communication technology are bringing many benefits to society, with transformative changes and financial opportunities being created in health care, transportation, education, law enforcement, national security, commerce, and social interactions. Many of these benefits, however, involve the use of sensitive personal data, and thereby raise concerns about privacy. Failure to address these concerns can lead to a loss of trust in the private and public institutions that handle personal data, and can stifle the independent thought and expression that is needed for our democracy to flourish. This report, sponsored by the Computing Community Consortium (CCC), suggests a roadmap for privacy research over the next decade, aimed at enabling society to appropriately control threats to privacy while enjoying the benefits of information technology and data science. We hope that it will be useful to the agencies of the Federal Networking and Information Technology Research and Development (NITRD) Program as they develop a joint National Privacy Research Strategy over the coming months. The report synthesizes input drawn from the privacy and computing communities submitted to both the CCC and NITRD, as well as past reports on the topic.
Learning Simple Auctions
Venue: arXiv cs.LG 2016
Year: 2016

We present a general framework for proving polynomial sample complexity bounds for the problem of learning from samples the best auction in a class of "simple" auctions. Our framework captures all of the most prominent examples of "simple" auctions, including anonymous and non-anonymous item and bundle pricings, with either a single or multiple buyers. The technique we propose is to break the analysis of auctions into two natural pieces. First, one shows that the set of allocation rules have large amounts of structure; second, fixing an allocation on a sample, one shows that the set of auctions agreeing with this allocation on that sample have revenue functions with low dimensionality. Our results effectively imply that whenever it's possible to compute a near-optimal simple auction with a known prior, it is also possible to compute such an auction with an unknown prior (given a polynomial number of samples).
Adaptive Caching Networks with Optimality Guarantees
Venue: arXiv cs.NI 2016
Year: 2016

We study the problem of optimal content placement over a network of caches, a problem naturally arising in several networking applications, including ICNs, CDNs, and P2P systems. Given a demand of content request rates and paths followed, we wish to determine the content placement that maximizes the expected caching gain, i.e., the reduction of routing costs due to intermediate caching. The offline version of this problem is NP-hard and, in general, the demand and topology may be a priori unknown. Hence, a distributed, adaptive, constant approximation content placement algorithm is desired. We show that path replication, a simple algorithm frequently encountered in literature, can be arbitrarily suboptimal when combined with traditional eviction policies, like LRU, LFU, or FIFO. We propose a distributed, adaptive algorithm that performs stochastic gradient ascent on a concave relaxation of the expected caching gain, and constructs a probabilistic content placement within 1-1/e factor from the optimal, in expectation. Motivated by our analysis, we also propose a novel greedy eviction policy to be used with path replication, and show through numerical evaluations that both algorithms significantly outperform path replication with traditional eviction policies over a broad array of network topologies.
Desiree - a Refinement Calculus for Requirements Engineering
Venue: arXiv cs.SE 2016
Year: 2016

The requirements elicited from stakeholders suffer from various afflictions, including informality, incompleteness, ambiguity, vagueness, inconsistencies, and more. It is the task of requirements engineering (RE) processes to derive from these an eligible (formal, complete enough, unambiguous, consistent, measurable, satisfiable, modifiable and traceable) requirements specification that truly captures stakeholder needs. We propose Desiree, a refinement calculus for systematically transforming stakeholder require-ments into an eligible specification. The core of the calculus is a rich set of requirements operators that iteratively transform stakeholder requirements by strengthening or weakening them, thereby reducing incompleteness, removing ambiguities and vagueness, eliminating unattainability and conflicts, turning them into an eligible specification. The framework also includes an ontology for modeling and classifying requirements, a description-based language for representing requirements, as well as a systematic method for applying the concepts and operators. In addition, we define the semantics of the requirements concepts and operators, and develop a graphical modeling tool in support of the entire framework. To evaluate our proposal, we have conducted a series of empirical evaluations, including an ontology evaluation by classifying a large public requirements set, a language evaluation by rewriting the large set of requirements using our description-based syntax, a method evaluation through a realistic case study, and an evaluation of the entire framework through three controlled experiments. The results of our evaluations show that our ontology, language, and method are adequate in capturing requirements in practice, and offer strong evidence that with sufficient training, our framework indeed helps people conduct more effective requirements engineering.
Privacy-Preserving Human Activity Recognition from Extreme Low Resolution
Venue: arXiv cs.CV 2016
Year: 2016

Privacy protection from surreptitious video recordings is an important societal challenge. We desire a computer vision system (e.g., a robot) that can recognize human activities and assist our daily life, yet ensure that it is not recording video that may invade our privacy. This paper presents a fundamental approach to address such contradicting objectives: human activity recognition while only using extreme low-resolution (e.g., 16x12) anonymized videos. We introduce the paradigm of inverse super resolution (ISR), the concept of learning the optimal set of image transformations to generate multiple low-resolution (LR) training videos from a single video. Our ISR learns different types of sub-pixel transformations optimized for the activity classification, allowing the classifier to best take advantage of existing high-resolution videos (e.g., YouTube videos) by creating multiple LR training videos tailored for the problem. We experimentally confirm that the paradigm of inverse super resolution is able to benefit activity recognition from extreme low-resolution videos.
Efficient Classification of Multi-Labelled Text Streams by Clashing
Venue: arXiv cs.AI 2016
Year: 2016

We present a method for the classification of multi-labelled text documents explicitly designed for data stream applications that require to process a virtually infinite sequence of data using constant memory and constant processing time. Our method is composed of an online procedure used to efficiently map text into a low-dimensional feature space and a partition of this space into a set of regions for which the system extracts and keeps statistics used to predict multi-label text annotations. Documents are fed into the system as a sequence of words, mapped to a region of the partition, and annotated using the statistics computed from the labelled instances colliding in the same region. This approach is referred to as clashing. We illustrate the method in real-world text data, comparing the results with those obtained using other text classifiers. In addition, we provide an analysis about the effect of the representation space dimensionality on the predictive performance of the system. Our results show that the online embedding indeed approximates the geometry of the full corpus-wise TF and TF-IDF space. The model obtains competitive F measures with respect to the most accurate methods, using significantly fewer computational resources. In addition, the method achieves a higher macro-averaged F measure than methods with similar running time. Furthermore, the system is able to learn faster than the other methods from partially labelled streams.
Recommendations for web service composition by mining usage logs
Venue: arXiv cs.SE 2016
Year: 2016

Web service composition has been one of the most researched topics of the past decade. Novel methods of web service composition are being proposed in the literature include Semantics-based composition, WSDLbased composition. Although these methods provide promising results for composition, search and discovery of web service based on QoS parameter of network and semantics or ontology associated with WSDL, they do not address composition based on usage of web service. Web Service usage logs capture time series data of web service invocation by business objects, which innately captures patterns or workflows associated with business operations. Web service composition based on such patterns and workflows can greatly streamline the business operations. In this research work, we try to explore and implement methods of mining web service usage logs. Main objectives include Identifying usage association of services. Linking one service invocation with other, Evaluation of the causal relationship between associations of services
Hippo: A Fast, yet Scalable, Database Indexing Approach
Venue: arXiv cs.DB 2016
Year: 2016

Even though existing database indexes (e.g., B+-Tree) speed up the query execution, they suffer from two main drawbacks: (1) A database index usually yields 5% to 15% additional storage overhead which results in non-ignorable dollar cost in big data scenarios especially when deployed on modern storage devices like Solid State Disk (SSD) or Non-Volatile Memory (NVM). (2) Maintaining a database index incurs high latency because the DBMS has to find and update those index pages affected by the underlying table changes. This paper proposes Hippo a fast, yet scalable, database indexing approach. Hippo only stores the pointers of disk pages along with light weight histogram-based summaries. The proposed structure significantly shrinks index storage and maintenance overhead without compromising much on query execution performance. Experiments, based on real Hippo implementation inside PostgreSQL 9.5, using the TPC-H benchmark show that Hippo achieves up to two orders of magnitude less storage space and up to three orders of magnitude less maintenance overhead than traditional database indexes, i.e., B+-Tree. Furthermore, the experiments also show that Hippo achieves comparable query execution performance to that of the B+-Tree for various selectivity factors.
Optimal Route Planning with Prioritized Task Scheduling for AUV Missions
Venue: arXiv cs.RO 2016
Year: 2016

This paper presents a solution to Autonomous Underwater Vehicles (AUVs) large scale route planning and task assignment joint problem. Given a set of constraints (e.g., time) and a set of task priority values, the goal is to find the optimal route for underwater mission that maximizes the sum of the priorities and minimizes the total risk percentage while meeting the given constraints. Making use of the heuristic nature of genetic and swarm intelligence algorithms in solving NP-hard graph problems, Particle Swarm Optimization (PSO) and Genetic Algorithm (GA) are employed to find the optimum solution, where each individual in the population is a candidate solution (route). To evaluate the robustness of the proposed methods, the performance of the all PS and GA algorithms are examined and compared for a number of Monte Carlo runs. Simulation results suggest that the routes generated by both algorithms are feasible and reliable enough, and applicable for underwater motion planning. However, the GA-based route planner produces superior results comparing to the results obtained from the PSO based route planner.
Typical Stability
Venue: arXiv cs.LG 2016
Year: 2016

In this paper, we introduce a notion of algorithmic stability called typical stability. When our goal is to release real-valued queries (statistics) computed over a dataset, this notion does not require the queries to be of bounded sensitivity -- a condition that is generally assumed under differential privacy [DMNS06, Dwork06] when used as a notion of algorithmic stability [DFHPRR15a, DFHPRR15b, BNSSSU16] -- nor does it require the samples in the dataset to be independent -- a condition that is usually assumed when generalization-error guarantees are sought. Instead, typical stability requires the output of the query, when computed on a dataset drawn from the underlying distribution, to be concentrated around its expected value with respect to that distribution. We discuss the implications of typical stability on the generalization error (i.e., the difference between the value of the query computed on the dataset and the expected value of the query with respect to the true data distribution). We show that typical stability can control generalization error in adaptive data analysis even when the samples in the dataset are not necessarily independent and when queries to be computed are not necessarily of bounded-sensitivity as long as the results of the queries over the dataset (i.e., the computed statistics) follow a distribution with a "light" tail. Examples of such queries include, but not limited to, subgaussian and subexponential queries. We also discuss the composition guarantees of typical stability and prove composition theorems that characterize the degradation of the parameters of typical stability under $k$-fold adaptive composition. We also give simple noise-addition algorithms that achieve this notion. These algorithms are similar to their differentially private counterparts, however, the added noise is calibrated differently.
Locally Orthogonal Training Design for Cloud-RANs Based on Graph Coloring
Venue: arXiv cs.IT 2016
Year: 2016

We consider training-based channel estimation for a cloud radio access network (CRAN), in which a large amount of remote radio heads (RRHs) and users are randomly scattered over the service area. In this model, assigning orthogonal training sequences to all users will incur a substantial overhead to the overall network, and is even impossible when the number of users is large. Therefore, in this paper, we introduce the notion of local orthogonality, under which the training sequence of a user is orthogonal to those of the other users in its neighborhood. We model the design of locally orthogonal training sequences as a graph coloring problem. Then, based on the theory of random geometric graph, we show that the minimum training length scales in the order of $\ln K$, where $K$ is the number of users covered by a CRAN. This indicates that the proposed training design yields a scalable solution to sustain the need of large-scale cooperation in CRANs. Numerical results show that the proposed scheme outperforms other reference schemes.
Avoiding the Flip Ambiguities in 2D Wireless Sensor Localization by Using Unit Disk Graph Property
Venue: arXiv cs.NI 2016
Year: 2016

In this paper, we propose a range-based localization algorithm to localize a wireless sensor network (WSN) in 2D. A widely used algorithm to localize a WSN in 2D is trilateration, which runs in polynomial time. Trilateration uses three distance measurements to localize a node. In some cases, the lack of connectivity leads to a low percentage of localized nodes since a node's position can be fixed using three distance measurements. We propose an algorithm that finds the position of a node by using the absence of a distance measurement in addition to a third distance measurement. If two nodes are not able to sense each other, that means the distance between them is more than the sensing range. Therefore, our algorithm checks if the possible positions of an unlocalized node $u$ is inside the sensing range of a localized node $\ell$ that is not the neighbor of $u$. In such case, we eliminate one of the possible positions.